The Major Facilitator Superfamily (MFS) is the largest superfamily of secondary carriers known. It includes a few families of proteins that catalyze processes other than secondary transport. For example, evidence suggests that the Major Intrinsic Protein (MIP) family of aquaporins and glycerol channels is related to the MFS as are Rhomboid proteases and the glycosyl transferase (GT) superfamily (unpublished observations).
Chang A.B., Lin R., Studley W.K., Tran C.V., Saier M.H. Jr. 2004. Phylogeny as a Guide to Structure and Function of Membrane Transport Proteins. Mol Membr Biol. 21(3):171-81.
Reddy, V.S., M.A. Shlykov, R. Castillo, E.I. Sun, and M.H. Saier, Jr. (2012). The major facilitator superfamily (MFS) revisited. FEBS J. 279: 2022-2035.

as well as the ECF sub-superfamily are all included within the functional ABC superfamily, TC#3.A.1. Their descriptions and constituent families are presented in paragraphs 3 and 4 of the superfamily description under TC#3.A.1. The ABC2 uptake Superfamily includes proteins in TC families 2.A.87 (P-RFT) and 2.A.88 (VUT or ECF).

Glycosyl transferases can be integral membrane proteins with numerous TMSs that in some cases have been shown to transport the growing polysaccharide chain as it is being elongated in a group translocation process.

The Na+ pumping NQR (3.D.5) and RNF (3.D.6) families include protein complexes of six homologous but dissimilar subunits. Two of the six subunits, NqrD and NqrE, and RnfA and RnfD are homologous to each other. However, within 3.D.5 and 3.D.6, only one of the six protein constituents, NqrB and RnfD, respectively, is homologous to Urea Transporters (UT, 1.A.28), and these are believed to be responsible for Na+ transport.

Mrp of Bacillus subtilis is a 7 subunit Na+/H+ antiporter complex (2.A.63.1.4). All subunits are homologous to the subunits in other members of this monovalent cation (K+ or Na+): proton antiporter-3 (CPA3) family as well as subunits in the archaeal hydrogenases (3.D.1.4.1 and 3.D.1.4.2) which share many subunits with NADH dehydrogenase subunits (3.D.1). The largest subunit of the Mrp complex (Mrp A and Mrp D) are homologous to the subunits in NADH dehydrogenases (NDH, ND2, ND4 and ND5 in the fungal NADH dehydrogenase complex) and most other NDHs. (TC#3.D.1) as well are subunits in the F420H2 dehydrogenase of Methanosarcina mazei (TC#3.D.9.1.1). (Zickermann et al. 2015). New subunits in three TC families are homologous, and in all such systems, these subunits may function as Na+/K+ and/or H+ transporters.

Full length polyphosphate polymerases (TC# 4.E.1) have a C-terminal 3 TMS domain that is in the ubiquitous DUF202 domain/E. coli YidH protein Family (TC# 9.B.51). These small proteins, all with 3 TMSs, are found in bacteria, archaea and eukaryotes.

Pex11 of yeast has been shown to be a pore-forming protein (see TC# 1.A.101). It is homologous and similar in size to Pex25 and Pex27. All three proteins are constituents of the Peroxisomal Protein Importer (PPI) Family (see TC# 3.A.20.1.5).

Protein kinase domains are sometimes found in transport proteins. These include TC#s 1.A.87.2.1-6, 1.A.105.1.1, 1.I.1.1.3 (with four such proteins in this system), 9.A.15.1.1, 9.B.45.1.3 and 9.B.106.3.1-3. Some of these proteins have channel/transport domains distinct from the kinase domains.

The Bcl-2 Superfamily includes two families in TCDB, the Bcl-2 family (TC# 1.A.21), consisting of homologues, some of which form transmembrane pores, and the Bim Family (8.A.69), members of which influence apoptosis, either positively or negatively, and interact with TOM complex proteins (TC# 3.A.8).

Several proteins in TCDB contain one or two ~100 aa synaptotagmin domains that are involved in calcium and receptor signalling as well as intracellular lipid transport (Pinheiro et al., 2016; PMID# 27731902).

These ATPase are found as coomponents of several protein secretion systems as well as synaptosomal fusion systems. All of these systems are multi-component systems where the ATPases play energizing roles. See Miller JM, Enemark EJ., Fundamental Characteristics of AAA+ Protein Family Structure and Function. Archaea. 2016 PMID: 27703410.

This superfamily includes Calcium binding domains and proteins of about 220 aas. Many proteins in the Phox family (5.B.1) have N-terminal domains of about 220 aas that are homologous to the members of the calmodulin family (TC# 8.A.82). Other proteins bearing this domain include Mitochondrial Carriers (TC# 2.A.29.23.1, 8 and 9) and the Programmed Cell Death 8 protein (O75340; TC# 3.A.5.9.1).

The multi-component families listed under this superfamily share several constituents, and all are included in subfamily 5.B. However, two other families, 5.A.3 and 3.D.7, contain constituents that are homologous to some of these proteins.